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The simulation platform focused on what matters to you.

Computational biology reimagined.

Geppetto is a web-based multi-algorithm, multi-scale simulation platform engineered to support the simulation of complex biological systems and their surrounding environment.

A completely modular platform.

Engineered together with scientists, Geppetto lets you integrate different simulators and models. Independent modules allow the user to read different standard modeling formats and to simulate different aspects of reality.

An open-source revolution.

Geppetto is entirely open source and engineers, scientists and developers are welcome to contribute to its development by adding functionality to existing modules or by creating new ones!

Features

Some of the features responsible for giving you an amazing experience.

Help us identify what matters to you and what you would want to see built in Geppetto. Do so by logging an enhancement request on GitHub or dropping us an email.

Curious to know more about Geppetto?

Get involved!

Help us building the next generation simulation platform!

Geppetto is entirely open source and is being built by a growing community of talented engineers and scientists. Geppetto uses different languages to achieve different goals. Its core and back-end are built in Java to provide a solid and performant infrastructure. The front-end is built using the latest HTML5 and Javascript awesome. A module to support scientists to write Python code to script it is also being built. Geppetto is being developed using the Eclipse platform and uses technologies like OSGi, Spring Framework, OpenCL and Maven. Geppetto's front-end is written using THREE.js and WebGL. The back-end and the front-end communicate by exchanging JSON messages through WebSocket. Geppetto runs on the Eclipse Virgo WebServer and can be deployed on different infrastructures including cloud-based ones like Amazon EC2. Anything sound familiar?

Geppetto is multi-platform and works on Linux, Mac OsX and Windows, so no matter on what platform you develop there is a way for you to run it and add fantastic contributions.

Show me the code!

Right! Geppetto is hosted on GitHub as you would expect. Every module has its own repository to provide flexible ways of branching individual components. For every module we have at least two branches, development and master. The development branch gets merged into master each monthly release. If you want to contribute you can either go straight to the code or reach out to us dropping an email, we will show you around and help you contribute in your favorite way!

Source code Docs

F.A.Q.

Find some answers to the most common questions about Geppetto!

Beside the functional requirements, Geppetto's goal is to move away from the monolithic approach to software that is usually found in academic programming projects.

Computational neuroscience has produced software systems, including NEURON and Genesis, that are extremely useful for simulating systems of neurons that include biophysical details (Brette et al, 2007). A range of other algorithms have been devised in other areas of computational biology (Barnes & Chu, 2010) for which simulators have been produced (Takahashi, 2004). Several investigations have pointed to the challenges in building a single system that integrates multiple simulation algorithms together into a single biological model (Takahashi et al., 2002, Dada and Mendes, 2007, Cornelis et al., 2012).

Geppetto aims to address these scientific and engineering challenges. Geppetto's design leverages cutting edge software technologies. Its architecture and development follows industry standards.

Building great software takes time. And money. Geppetto is no exception and as many open-source projects it is funded by a hybrid model. Geppetto's development is supported by both awesome volunteer contributors and by external companies and organisations:

Commercial companies, academic institutions and independent research labs are welcome to get in touch with us to discuss collaborations and grant applications.

The decision to build Geppetto came after an analysis of the requirements for a platform able to support the OpenWorm full-scale simulation of the C. elegans.

Geppetto's architecture is generic and therefore the simulation of the C.elegans is just one specific simulation it is capable of. Geppetto's modules can be built to simulate and integrate any complex system.

Geppetto is released under the MIT license.

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